Single Molecule Method for Molecular Biology

Jeong Hee Kim,Cherlhyun Jeong 대한구강생물학회 2018 International Journal of Oral Biology Vol.43 No.2

In order to understand biological phenomena accurately, single molecule techniques using a physical research approach to molecular interactions have been developed, and are now widely being used to study complex biological processes. In this review, we discuss some of the single molecule methods which are composed of two major parts: single molecule spectroscopy and manipulation. In particular, we explain how these techniques work and introduce the current research which uses them. Finally, we present the oral biology research using the single molecule methods.

Facile fabrication and application of near-IR light-responsive drug release system based on gold nanorods and phase change material

Lee, Junseok,Jeong, Cherlhyun,Kim, Won Jong The Royal Society of Chemistry 2014 Journal of Materials Chemistry B Vol.2 No.47

ATP Alters the Diffusion Mechanics of MutS on Mismatched DNA

Cho, Won-Ki,Jeong, Cherlhyun,Kim, Daehyung,Chang, Minhyeok,Song, Kyung-Mi,Hanne, Jeungphill,Ban, Changill,Fishel, Richard,Lee, Jong-Bong Elsevier 2012 Structure Vol.20 No.7

<P><B>Summary</B></P><P>The mismatch repair (MMR) initiation protein MutS forms at least two types of sliding clamps on DNA: a transient mismatch searching clamp (∼1 s) and an unusually stable (∼600 s) ATP-bound clamp that recruits downstream MMR components. Remarkably, direct visualization of single MutS particles on mismatched DNA has not been reported. We have combined real-time particle tracking with fluorescence resonance energy transfer (FRET) to image MutS diffusion dynamics on DNA containing a single mismatch. We show searching MutS rotates during diffusion independent of ionic strength or flow rate, suggesting continuous contact with the DNA backbone. In contrast, ATP-bound MutS clamps that are visually and successively released from the mismatch spin freely around the DNA, and their diffusion is affected by ionic strength and flow rate. These observations show that ATP binding alters the MutS diffusion mechanics on DNA, which has a number of implications for the mechanism of MMR.</P> <P><B>Graphical Abstract</B></P><P><ce:figure id='dfig1'></ce:figure></P><P><B>Highlights</B></P><P>► The development and use of smFlow-FRET and smPolarization-TIRF microscopy ► Lesion-searching MutS rotationally diffuses in continuous contact with the DNA ► ATP-bound MutS spins freely and in discontinuous contact with the DNA backbone ► Direct visualization of multiple ATP-bound MutS clamps that diffuse along the DNA</P>

Thermal analysis of self-heating in saddle MOSFET devices

Oh, Hyun Gon,Jeong, Cherlhyun,Cho, Il Hwan IOP Publishing 2014 Japanese journal of applied physics Vol.53 No.2

<P>The self-heating effects (SHEs) of saddle metal oxide semiconductor field-effect transistors (MOSFETs) and gate dimensional impacts on thermal characteristics have been investigated on the basis of a realistic thermal conductivity of silicon and other materials. Thermal characteristics were analyzed by thermal resistance of Si channel. Since Si material has larger thermal conductivity than that of silicon dioxide, it is shown that the length of the side gate of saddle MOSFETs determines heat dissipation of Si channel. Side gate of saddle MOSFETs can be one of the important parameter in device optimization. (C) 2014 The Japan Society of Applied Physics</P>

Topographic control of lipid-raft reconstitution in model membranes

Yoon, Tae-Young,Jeong, Cherlhyun,Lee, Sang-Wook,Kim, Joon Heon,Choi, Myung Chul,Kim, Sung-Jin,Kim, Mahn Won,Lee, Sin-Doo Nature Publishing Group 2006 NATURE MATERIALS Vol.5 No.4

Liquid-ordered (L<SUB>O</SUB>) domains reconstituted in model membranes have provided a useful platform for in vitro studies of the lipid-raft model, in which signalling membrane molecules are thought to be compartmentalized in sphingolipid- and cholesterol-rich domains. These in vitro studies, however, have relied on an uncontrolled phase-separation process that gives a random distribution of L<SUB>O</SUB> domains. Obviously, a precise control of the size and spatial distribution of the L<SUB>O</SUB> domains would enable a more systematic large-scale in vitro study of the lipid-raft model. The prerequisite for such capability would be the generation of a well-defined energy landscape for reconstituting the L<SUB>O</SUB> domain without disrupting the two-dimensional (2D) fluidity of the model membrane. Here we report controlling the reconstitution of the L<SUB>O</SUB> domains in a spatially selective manner by predefining a landscape of energy barriers using topographic surface modifications. We show that the selective reconstitution spontaneously arises from the 2D brownian motion of nanoscale L<SUB>O</SUB> domains and signalling molecules captured in these nanodomains, which in turn produce a prescribed, concentrated downstream biochemical process. Our approach opens up the possibility of engineering model biological membranes by taking advantage of the intrinsic 2D fluidity. Moreover, our results indicate that the topographic configuration of cellular membranes could be an important machinery for controlling the lipid raft in vivo.

Scaling Down Characteristics of Vertical Channel Phase Change Random Access Memory (VPCRAM)

Chun Woong Park,Chongdae Park,Woo Young Choi,Dongsun Seo,Cherlhyun Jeong,Il Hwan Cho 대한전자공학회 2014 Journal of semiconductor technology and science Vol.14 No.1

In this paper, scaling down characteristics of vertical channel phase random access memory are investigated with device simulator and finite element analysis simulator. Electrical properties of select transistor are obtained by device simulator and those of phase change material are obtained by finite element analysis simulator. From the fusion of both data, scaling properties of vertical channel phase change random access memory (VPCRAM) are considered with ITRS roadmap. Simulation of set reset current are carried out to analyze the feasibility of scaling down and compared with values in ITRS roadmap. Simulation results show that width and length ratio of the phase change material (PCM) is key parameter of scaling down in VPCRAM. Thermal simulation results provide the design guideline of VPCRAM. Optimization of phase change material in VPCRAM can be achieved by oxide sidewall process optimization.

Scaling Down Characteristics of Vertical Channel Phase Change Random Access Memory (VPCRAM)

Park, Chun Woong,Park, Chongdae,Choi, Woo Young,Seo, Dongsun,Jeong, Cherlhyun,Cho, Il Hwan The Institute of Electronics and Information Engin 2014 Journal of semiconductor technology and science Vol.14 No.1

In this paper, scaling down characteristics of vertical channel phase random access memory are investigated with device simulator and finite element analysis simulator. Electrical properties of select transistor are obtained by device simulator and those of phase change material are obtained by finite element analysis simulator. From the fusion of both data, scaling properties of vertical channel phase change random access memory (VPCRAM) are considered with ITRS roadmap. Simulation of set reset current are carried out to analyze the feasibility of scaling down and compared with values in ITRS roadmap. Simulation results show that width and length ratio of the phase change material (PCM) is key parameter of scaling down in VPCRAM. Thermal simulation results provide the design guideline of VPCRAM. Optimization of phase change material in VPCRAM can be achieved by oxide sidewall process optimization.

DLS-based fusion assay of SNARE-driven membrane fusion

Yoosoo YANG,Paul HEO,Byoung-Jae KONG,Jun-bum PARK,Young-Hun JUNG,Jonghyeok SHIN,Cherlhyun JEONG,Dae-Hyuk KWEON 한국생물공학회 2016 한국생물공학회 학술대회 Vol.2016 No.4

Ferritin nanocage with intrinsically disordered proteins and affibody: A platform for tumor targeting with extended pharmacokinetics

Lee, Na Kyeong,Lee, Eun Jung,Kim, Soyoun,Nam, Gi-hoon,Kih, Minwoo,Hong, Yeonsun,Jeong, Cherlhyun,Yang, Yoosoo,Byun, Youngro,Kim, In-San Elsevier 2017 Journal of controlled release Vol.267 No.-

<P><B>Abstract</B></P> <P>Ferritin nanocages are of particular interest as a novel platform for drug and vaccine delivery, diagnosis, biomineralization scaffold and more, due to their perfect and complex symmetry, ideal physical properties, high biocompatibility, low toxicity profiles as well as easy manipulation by genetic or chemical strategies. However, a short half-life is still a hurdle for the translation of ferritin-based nanomedicines into the clinic. Here, we developed a series of rationally designed long circulating ferritin nanocages (LCFNs) with ‘Intrinsically Disordered Proteins (IDP)’ as a stealth layer for extending the half-life of ferritin nanocages. Through predictions with 3D modelling, the LCFNs were designed, generated and their pharmacokinetic parameters including half-life, clearance rate, mean residence time, and more, were evaluated by qualitative and quantitative analysis. LCFNs have a tenfold increased half-life and overall improved pharmacokinetic parameters compared to wild-type ferritin nanocages (wtFN), corresponding to the low binding against bone marrow-derived macrophages (BMDMs) and endothelial cells. Subsequently, a tumor targeting moiety, epidermal growth factor receptor (EGFR)-targeting affibody peptide, was fused to LCFNs for evaluating their potential as a theragnostic platform. The tumor targeting-LCFNs successfully accumulated to the tumor tissue, by efficient targeting <I>via</I> active and passive properties, and also the shielding effect of IDP <I>in vivo</I>. This strategy can be applied to other protein-based nanocages for further progressing their use in the field of nanomedicine.</P> <P><B>Graphical abstract</B></P> <P>Long circulating ferritin nanocages are designed by 3D modelling. Modified by intrinsically disordered protein (IDP) clouds, this novel biocompatible nanocage platform can be applied in the field of nanomedicine.</P> <P>[DISPLAY OMISSION]</P>

Designed trimer-mimetic TNF superfamily ligands on self-assembling nanocages

Kih, Minwoo,Lee, Eun Jung,Lee, Na Kyeong,Kim, Yoon Kyoung,Lee, Kyung Eun,Jeong, Cherlhyun,Yang, Yoosoo,Kim, Dong-Hwee,Kim, In-San Elsevier 2018 Biomaterials Vol.180 No.-

<P><B>Abstract</B></P> <P>Presentation of an endogenous bioactive ligand in its native form is a key factor in controlling and determining its bioactivity, stability, and therapeutic efficacy. In this study, we developed a novel strategy for presenting trimeric ligands on nanocages by designing, optimizing and testing based on the rational design, high-resolution structural analysis and agonistic activity assays <I>in vitro</I> and <I>in vivo</I>. We successfully designed a nanocage that presents the TNF superfamily member, TRAIL (TNF-related apoptosis-inducing ligand) in its native-like trimeric structure. The native structure of TRAIL complexes was mimicked on the resulting trimeric TRAIL-presenting nanocages (TTPNs) by inserting sufficient spacing, determined from three-dimensional structural models, to provide optimal access to the corresponding receptors. The efficacy of TTPNs as an anti-tumor agent was confirmed in preclinical studies, which revealed up to 330-fold increased affinity, 62.5-fold enhanced apoptotic activity, and improved pharmacokinetic characteristics and stability compared with the monomeric form of TRAIL (mTRAIL). In this latter context, TTPNs exhibited greater than 90% stability over 1 mo, whereas ∼50% of mTRAIL aggregated within 2 d. Consistent with their enhanced stability and ultra-high affinity for the TRAIL receptor, TTPNs effectively induced apoptosis of tumor cells <I>in vivo</I>, leading to effective inhibition of tumor growth. Although TRAIL was used here as a proof-of-concept, all members of the TNF superfamily share the TNF homology domain (THD) and have similar distances between ecto-domain C-termini. Thus, other TNF superfamily ligands could be genetically substituted for the TRAIL ligand on the surface of this biomimetic delivery platform.</P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>